4S24
1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 295 | Protein: 10.2 mg/ml, 0.1M Tris HCl (pH 8.3), Screen: JSCG+ (C6), 0.1M Phosphate-citrate (pH 4.2), 40% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.76 | 55.48 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 72.046 | α = 90 |
b = 72.046 | β = 90 |
c = 166.766 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | beryllium lenses | 2014-12-11 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 1.7 | 30 | 99.9 | 0.067 | 0.067 | 62.5 | 15.2 | 29069 | 29069 | -3 | 25.7 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.7 | 1.73 | 100 | 0.56 | 0.56 | 6.2 | 15.5 | 1417 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 1.7 | 29.41 | 27589 | 27589 | 1407 | 99.92 | 0.14937 | 0.14852 | 0.16591 | RANDOM | 33.702 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.81 | 0.41 | 0.81 | -2.64 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.06 |
r_dihedral_angle_4_deg | 18.773 |
r_dihedral_angle_3_deg | 9.683 |
r_long_range_B_refined | 7.212 |
r_long_range_B_other | 6.98 |
r_scangle_other | 3.992 |
r_dihedral_angle_1_deg | 3.941 |
r_mcangle_it | 2.784 |
r_mcangle_other | 2.784 |
r_scbond_it | 2.641 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1531 |
Nucleic Acid Atoms | |
Solvent Atoms | 175 |
Heterogen Atoms | 45 |
Software
Software | |
---|---|
Software Name | Purpose |
Blu-Ice | data collection |
SHELXS | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |